It says that it couldn't open rh.orig.nofix and lh.orig.nofix. On the popup image, it doesn't look like the skull is present, but it does look like the cerebellum is. ________________________________________ From: Allison Stevens Player [astevens@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 1:28 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] "cannot allocate memory" issue
You can do: tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix
When you downloaded FreeSurfer, you would have also received the subject "bert" who is a good example to compare to. He will likely be located in: $FREESURFER_HOME/subjects/bert
If you do the same command above for bert: tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix
You'll see what the filled.mgz should look like. Allison
On Mon, 14 May 2012, Borzello, Mia wrote:
How do I check this? (Apologies for my ignorance.) So I might need to just use a different set of dicoms then?
thanks, Mia ________________________________________ From: Allison Stevens Player [astevens@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 1:02 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] "cannot allocate memory" issue
It looks like there is too huge a topology error for it to continue:
CORRECTING DEFECT 23 (vertices=143258, convex hull=19937) Excessive topologic defect encountered: could not allocate -729782272 edges for retessellation Cannot allocate memory
I would suggested looking at the filled.mgz to make sure skull and/or cerebellum are not included. Allison
On Mon, 14 May 2012, Borzello, Mia wrote:
Hi all,
I was wondering if you could help me figure out why the recon isn't running to completion. I've attached the log file (recon-all.log), but it's unclear to me what I should do to fix this problem. I tried to compute the lh.pial, but I guess it was never made in the recon.
Thanks so much, Mia